When changing the casing of a file, git does (under certain circumstances) not recognize the changes. To get the changes checked in, there is a simple workaround.
Assuming the file Myfile.txt was changed to myfile.txt, you can

  1. Rename the file to something entirely new (mv myfile.txt myfile_tmp.txt)
  2. Check that new file in (git add myfile_tmp.txt)
  3. Name the file back to the originally intended name (mv myfile_tmp.txt myfile.txt)
  4. Check the file in again (git add myfile.txt)

Git should now recognize the changed casing in the filename.